5MU8

HUMAN TNF-ALPHA IN COMPLEX WITH JNJ525


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.300 (Depositor), 0.300 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted JNIClick on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

Structural Basis of Small-Molecule Aggregate Induced Inhibition of a Protein-Protein Interaction.

Blevitt, J.M.Hack, M.D.Herman, K.L.Jackson, P.F.Krawczuk, P.J.Lebsack, A.D.Liu, A.X.Mirzadegan, T.Nelen, M.I.Patrick, A.N.Steinbacher, S.Milla, M.E.Lumb, K.J.

(2017) J Med Chem 60: 3511-3517

  • DOI: https://doi.org/10.1021/acs.jmedchem.6b01836
  • Primary Citation of Related Structures:  
    5MU8

  • PubMed Abstract: 

    A prevalent observation in high-throughput screening and drug discovery programs is the inhibition of protein function by small-molecule compound aggregation. Here, we present the X-ray structural description of aggregation-based inhibition of a protein-protein interaction involving tumor necrosis factor α (TNFα). An ordered conglomerate of an aggregating small-molecule inhibitor (JNJ525) induces a quaternary structure switch of TNFα that inhibits the protein-protein interaction between TNFα and TNFα receptors. SPD-304 may employ a similar mechanism of inhibition.


  • Organizational Affiliation

    Emerging Science & Innovation, Discovery Sciences, Janssen R&D LLC , La Jolla, California 92121, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tumor necrosis factor159Homo sapiensMutation(s): 0 
Gene Names: TNFTNFATNFSF2
UniProt & NIH Common Fund Data Resources
Find proteins for P01375 (Homo sapiens)
Explore P01375 
Go to UniProtKB:  P01375
PHAROS:  P01375
GTEx:  ENSG00000232810 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01375
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JNI
Query on JNI

Download Ideal Coordinates CCD File 
AB [auth D]
AC [auth h]
BB [auth F]
BC [auth h]
CB [auth F]
~{N}4-(phenylmethyl)-~{N}4-[2-[3-(2-piperazin-1-ylpyrimidin-5-yl)phenyl]phenyl]pyrimidine-2,4-diamine
C31 H30 N8
FRBABIFCTILEGV-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
JNI BindingDB:  5MU8 IC50: min: 1100, max: 1200 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.300 (Depositor), 0.300 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.888α = 97.57
b = 118.348β = 94.31
c = 186.747γ = 98.75
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted JNIClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-29
    Type: Initial release
  • Version 1.1: 2017-04-12
    Changes: Database references
  • Version 1.2: 2017-05-10
    Changes: Database references
  • Version 1.3: 2019-02-20
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.4: 2024-11-13
    Changes: Data collection, Database references, Structure summary